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Single molecule force spectroscopy probes the strength, lifetime, and energetic details of intermolecular interactions in a simple experiment. A growing number of these studies have reported distinctly nonlinear trends in rupture force with loading rate that are typically explained in conventional models by invoking complex escape pathways. Recent analyses suggested that these trends should be expected even for simple barriers based on the basic assumptions of bond rupture dynamics and thus may represent the norm rather than the exception. Here we explore how these nonlinear trends reflect the two fundamental regimes of bond rupture: (i) a near-equilibrium regime, produced either by bond reforming in the case of a single bond or by asynchronized rupture of multiple individual bonds, and (ii) a kinetic regime produced by fast, non-equilibrium bond rupture. We analyze both single-and multibonded cases, describe the full evolution of the system as it transitions between near-and far-from-equilibrium loading regimes, and show that both interpretations produce essentially identical force spectra. Data from 10 different molecular systems show that this model provides a comprehensive description of force spectra for a diverse suite of bonds over experimentally relevant loading rates, removes the inconsistencies of previous interpretations of transition state distances, and gives ready access to both kinetic and thermodynamic information about the interaction. These results imply that single-molecule binding free energies for a vast number of bonds have already been measured.

Layered boron compounds have attracted significant interest in applications from energy storage to electronic materials to device applications, owing in part to a diversity of surface properties tied to specific arrangements of boron atoms. Here we report the energy landscape for surface atomic configurations of MgB 2 by combining first-principles calculations, global optimization, material synthesis and characterization. We demonstrate that contrary to previous assumptions, multiple disordered reconstructions are thermodynamically preferred and kinetically accessible within exposed B surfaces in MgB 2 and other layered metal diborides at low boron chemical potentials. Such a dynamic environment and intrinsic disordering of the B surface atoms present new opportunities to realize a diverse set of 2D boron structures. We validated the predicted surface disorder by characterizing exfoliated boron-terminated MgB 2 nanosheets. We further discuss application-relevant implications, with a particular view towards understanding the impact of boron surface heterogeneity on hydrogen storage performance. Layered boron compounds attract enormous interest in applications. This work reports first-principles calculations coupled with global optimization to show that the outer boron surface in MgB 2 nanosheets undergo disordering and clustering, which is experimentally confirmed in synthesized MgB 2 nanosheets.

Multivalent interactions play a critical role in a variety of biological processes on both molecular and cellular levels. We have used molecular force spectroscopy to investigate the strength of multiple parallel peptide-antibody bonds using a system that allowed us to determine the rupture forces and the number of ruptured bonds independently. In our experiments the interacting molecules were attached to the surfaces of the probe and sample of the atomic force microscope with flexible polymer tethers, and the unique mechanical signatures of the tethers determined the number of ruptured bonds. We show that the rupture forces increase with the number of interacting molecules and that the measured forces obey the predictions of a Markovian model for the strength of multiple parallel bonds. We also discuss the implications of our results to the interpretation of force spectroscopy measurements in multiple bond systems.

We used atomic force microscopy to measure the binding forces between Mucini (MUC1) peptide and a single-chain variable fragment (scFv) antibody selected from a scFv library screened against MUC1. This binding interaction is central to the design of molecules used for targeted delivery of radioimmunotherapeutic agents for prostate and breast cancer treatment. Our experiments separated the specific binding interaction from nonspecific interactions by tethering the antibody and MUC1 molecules to the atomic force microscope tip and sample surface with flexible polymer spacers. Rupture force magnitude and elastic characteristics of the spacers allowed identification of the rupture events corresponding to different numbers of interacting proteins. We used dynamic force spectroscopy to estimate the intermolecular potential widths and equivalent thermodynamic off rates for monovalent, bivalent, and trivalent interactions. Measured interaction potential parameters agree with the results of molecular docking simulation. Our results demonstrate that an increase of the interaction valency leads to a precipitous decline in the dissociation rate. Binding forces measured for monovalent and multivalent interactions match the predictions of a Markovian model for the strength of multiple uncorrelated bonds in a parallel configuration. Our approach is promising for comparison of the specific effects of molecular modifications as well as for determination of the best configuration of antibody-based multivalent targeting agents.

We developed a method for examining ice formation on solid substrates exposed to cloud-like atmospheres. Our experimental approach couples video-rate optical microscopy of ice formation with high-resolution atomic-force microscopy (AFM) of the initial mineral surface. We demonstrate how colocating stitched AFM images with video microscopy can be used to relate the likelihood of ice formation to nanoscale properties of a mineral substrate, e.g., the abundance of surface steps of a certain height. We also discuss the potential of this setup for future iterative investigations of the properties of ice nucleation sites on materials.

We used high-resolution atomic force microscopy to image the compaction of linear and circular DNA by the yeast mitochondrial protein Abf2p, which plays a major role in packaging mitochondrial DNA. Atomic force microscopy images show that protein binding induces drastic bends in the DNA backbone for both linear and circular DNA. At a high concentration of Abf2p DNA collapses into a tight nucleoprotein complex. We quantified the compaction of linear DNA by measuring the end-to-end distance of the DNA molecule at increasing concentrations of Abf2p. We also derived a polymer statistical mechanics model that provides a quantitative description of compaction observed in our experiments. This model shows that sharp bends in the DNA backbone are often sufficient to cause DNA compaction. Comparison of our model with the experimental data showed excellent quantitative correlation and allowed us to determine binding characteristics for Abf2p. These studies indicate that Abf2p compacts DNA through a simple mechanism that involves bending of the DNA backbone. We discuss the implications of such a mechanism for mitochondrial DNA maintenance and organization.

Carbon nanotubes 1 display a consummate blend of materials properties that affect applications ranging from nanoelectronic circuits 2 and biosensors 3 to field emitters 4 and membranes 5 . These applications use the non-covalent interactions between the nanotubes and chemical functionalities 6 , often involving a few molecules at a time. Despite their wide use, we still lack a fundamental understanding and molecular-level control of these interactions. We have used chemical force microscopy 7 to measure the strength of the interactions of single chemical functional groups with the sidewalls of vapour-grown individual single-walled carbon nanotubes. Surprisingly, the interaction strength does not follow conventional trends of increasing polarity or hydrophobicity, and instead reflects the complex electronic interactions between the nanotube and the functional group. Ab initio calculations confirm the observed trends and predict binding force distributions for a single molecular contact that match the experimental results. Our analysis also reveals the important role of molecular linkage dynamics in determining interaction strength at the single functional group level.

Higher organisms as well as medical and technological materials exploit mineral-polymer interactions, however, mechanistic understanding of these interactions is poorly constrained. Dynamic force spectroscopy can probe the free energy landscape of interacting bonds, but interpretations are challenged by the complex mechanical behavior of polymers. Here we restate the difficulties inherent to applying DFS to polymer-linked adhesion and present an approach to gain quantitative insight into polymer-mineral binding.

We develop a stochastic kinetic model of a pre-formed attachment of a mictrotuble (MT) with a cell cortex, in which the MT is tethered to the cell by a group of active motor proteins. Such an attachment is a particularly unique case of ligand-receptor bonds: The MT ligand changes its length (and thus binding sites) with time by polymerization-depolymerization kinetics, while multiple motor receptors tend to walk actively along the MT length. These processes, combined with force-mediated unbinding of the motors, result in an elaborate behavior of the MT connection to the cell cortex. We present results for the strength and lifetime of the system through the well-established force-clamp and force-ramp protocols when external tension is applied to the MT. The simulation results reveal that the MT-cell attachment behaves as a catch-bond or slip-bond depending on system parameters. We provide analytical approximations of the lifetime and discuss implications of our results on in-vitro experiments.